PIPSA - compare electrostatic interaction properties

Template input file used for UHBD calculations

All constructs of the form @{xyz}, or $xyz will be replaced by details concerning the respective calculation.

! This is a template UHBD input
! It is read and rewritten by program makuhbdin.f
! In order to not impair execution of this program you may introduce reasonable
! changes here except the lines beginning with ! and not place any
! assignments after the line ""! The end of assignments"
! Note that the program only overwrites the ionic strenth (ios) and
! xc, yc, zc values after the line "! The end of assignments"

assign dim    =  @{gridSize} end
assign ios    =   50 end
assign tmp    =   end
assign spa    =  1.0 end
assign rio    =  1.5 end
assign pd     =  2.0 end
assign sd     =  78  end
assign xc     =  0.000 end
assign yc     =  0.000 end
assign zc     =  0.000 end

! The end of assignments
! The end of re-assignments

read
    mol 1
    file "@{inputPdb}"
    fpdb
end

edit
   all radius equals 1.0
end
edit
   all charges equals 0
end

set
    charge
    radius
    param opls
    file "qtable.dat"
end
print apar mol1 end

elec
    mol1
    gcenter  $xc $yc $zc
    dime $dim $dim $dim
    pdie $pd
    sdie $sd
    bcfl 2
    ionstr $ios
    temp $tmp
    rion $rio
    spacing $spa
end

edit all radi shift 1.4 end
write phi file "@{outputGrd}" binary end
write phi file "@{outputGrd}_zero_inside.grid" binary exclude end

stop

webPIPSA Protein Interaction Property Similarity Analysis

Template input file used for UHBD calculations

webPIPSA

Protein Interaction Property Similarity Analysis